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Zhang W, Fan X, Gao Y, Liu L, Sun L, Su Q, Han J, Zhang N, Cui F, Ji J, Tong Y, Li J. Chromatin modification contributes to the expression divergence of three TaGS2 homoeologs in hexaploid wheat. Sci Rep 2017; 7:44677. [PMID: 28300215 PMCID: PMC5353557 DOI: 10.1038/srep44677] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/13/2017] [Indexed: 01/05/2023] Open
Abstract
Plastic glutamine synthetase (GS2) is responsible for ammonium assimilation. The reason that TaGS2 homoeologs in hexaploid wheat experience different selection pressures in the breeding process remains unclear. TaGS2 were minimally expressed in roots but predominantly expressed in leaves, and TaGS2-B had higher expression than TaGS2-A and TaGS2-D. ChIP assays revealed that the activation of TaGS2-B expression in leaves was correlated with increased H3K4 trimethylation. The transcriptional silencing of TaGS2 in roots was correlated with greater cytosine methylation and less H3K4 trimethylation. Micrococcal nuclease and DNase I accessibility experiments indicated that the promoter region was more resistant to digestion in roots than leaves, which indicated that the closed nucleosome conformation of the promoter region was important to the transcription initiation for the spatial-temporal expression of TaGS2. In contrast, the transcribed regions possess different nuclease accessibilities of three TaGS2 homoeologs in the same tissue, suggesting that nucleosome conformation of the transcribed region was part of the fine adjustment of TaGS2 homoeologs. This study provides evidence that histone modification, DNA methylation and nuclease accessibility coordinated the control of the transcription of TaGS2 homoeologs. Our results provided important evidence that TaGS2-B experienced the strongest selection pressures during the breeding process.
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Affiliation(s)
- Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Yingjie Gao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang 050024, China
| | - Lei Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Lijing Sun
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, China
| | - Qiannan Su
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fa Cui
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Chinese Academy of Sciences, Beijing 100101, China
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Jiang J. The 'dark matter' in the plant genomes: non-coding and unannotated DNA sequences associated with open chromatin. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:17-23. [PMID: 25625239 DOI: 10.1016/j.pbi.2015.01.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 01/12/2015] [Accepted: 01/13/2015] [Indexed: 05/03/2023]
Abstract
Sequencing of complete plant genomes has become increasingly more routine since the advent of the next-generation sequencing technology. Identification and annotation of large amounts of noncoding but functional DNA sequences, including cis-regulatory DNA elements (CREs), have become a new frontier in plant genome research. Genomic regions containing active CREs bound to regulatory proteins are hypersensitive to DNase I digestion and are called DNase I hypersensitive sites (DHSs). Several recent DHS studies in plants illustrate that DHS datasets produced by DNase I digestion followed by next-generation sequencing (DNase-seq) are highly valuable for the identification and characterization of CREs associated with plant development and responses to environmental cues. DHS-based genomic profiling has opened a door to identify and annotate the 'dark matter' in sequenced plant genomes.
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Affiliation(s)
- Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Roy D, Paul A, Roy A, Ghosh R, Ganguly P, Chaudhuri S. Differential acetylation of histone H3 at the regulatory region of OsDREB1b promoter facilitates chromatin remodelling and transcription activation during cold stress. PLoS One 2014; 9:e100343. [PMID: 24940877 PMCID: PMC4062490 DOI: 10.1371/journal.pone.0100343] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 05/25/2014] [Indexed: 11/26/2022] Open
Abstract
The rice ortholog of DREB1, OsDREB1b, is transcriptionally induced by cold stress and over-expression of OsDREB1b results in increase tolerance towards high salt and freezing stress. This spatio-temporal expression of OsDREB1b is preceded by the change in chromatin structure at the promoter and the upstream region for gene activation. The promoter and the upstream region of OsDREB1b genes appear to be arranged into a nucleosome array. Nucleosome mapping of ∼700bp upstream region of OsDREB1b shows two positioned nucleosomes between −610 to −258 and a weakly positioned nucleosome at the core promoter and the TSS. Upon cold stress, there is a significant change in the nucleosome arrangement at the upstream region with increase in DNaseI hypersensitivity or MNase digestion in the vicinity of cis elements and TATA box at the core promoter. ChIP assays shows hyper-acetylation of histone H3K9 throughout the locus whereas region specific increase was observed in H3K14ac and H3K27ac. Moreover, there is an enrichment of RNA PolII occupancy at the promoter region during transcription activation. There is no significant change in the H3 occupancy in OsDREB1b locus negating the possibility of nucleosome loss during cold stress. Interestingly, cold induced enhanced transcript level of OsDREB1b as well as histone H3 acetylation at the upstream region was found to diminish when stressed plants were returned to normal temperature. The result indicates absolute necessity of changes in chromatin conformation for the transcription up-regulation of OsDREB1b gene in response to cold stress. The combined results show the existence of closed chromatin conformation at the upstream and promoter region of OsDREB1b in the transcription “off” state. During cold stress, changes in region specific histone modification marks promote the alteration of chromatin structure to facilitate the binding of transcription machinery for proper gene expression.
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Affiliation(s)
- Dipan Roy
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Amit Paul
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Adrita Roy
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Ritesh Ghosh
- School of Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Payel Ganguly
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
| | - Shubho Chaudhuri
- Division of Plant Biology, Bose Institute (Centenary Campus), P-1/12, C.I.T. Scheme VII M, Kolkta-700054, West Bengal, India
- * E-mail:
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Ricardi MM, González RM, Iusem ND. Protocol: fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato. PLANT METHODS 2010; 6:11. [PMID: 20380723 PMCID: PMC2859366 DOI: 10.1186/1746-4811-6-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/09/2010] [Indexed: 05/19/2023]
Abstract
BACKGROUND Searching thoroughly for plant cis-elements corresponding to transcription factors is worthwhile to reveal novel gene activation cascades. At the same time, a great deal of research is currently focused on epigenetic events in plants. A widely used method serving both purposes is chromatin immunoprecipitation, which was developed for Arabidopsis and other plants but is not yet operational for tomato (Solanum lycopersicum), a model plant species for a group of economically important crops. RESULTS We developed a chromatin immunoprecipitation protocol suitable for tomato by adjusting the parameters to optimise in vivo crosslinking, purification of nuclei, chromatin extraction, DNA shearing and precipitate analysis using real-time PCR. Results were obtained with two different antibodies, five control loci and two normalisation criteria. CONCLUSION Here we provide a chromatin immunoprecipitation procedure for tomato leaves that could be combined with high-throughput sequencing to generate a detailed map of epigenetic modifications or genome-wide nucleosome positioning data.
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Affiliation(s)
- Martiniano M Ricardi
- Departamento de Fisiología, Biología Molecular y Celular. IFIByNE-CONICET. Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Rodrigo M González
- Departamento de Fisiología, Biología Molecular y Celular. IFIByNE-CONICET. Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Norberto D Iusem
- Departamento de Fisiología, Biología Molecular y Celular. IFIByNE-CONICET. Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
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Haring M, Offermann S, Danker T, Horst I, Peterhansel C, Stam M. Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization. PLANT METHODS 2007; 3:11. [PMID: 17892552 PMCID: PMC2077865 DOI: 10.1186/1746-4811-3-11] [Citation(s) in RCA: 384] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Accepted: 09/24/2007] [Indexed: 05/17/2023]
Abstract
BACKGROUND Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP). ChIP is widely used for a few model systems, including Arabidopsis, but establishment of the technique for other organisms is still remarkably challenging. Furthermore, quantitative analysis of the precipitated material and normalization of the data is often underestimated, negatively affecting data quality. RESULTS We developed a robust ChIP protocol, using maize (Zea mays) as a model system, and present a general strategy to systematically optimize this protocol for any type of tissue. We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. We experienced that the use of quantitative PCR (QPCR) is crucial for obtaining high quality ChIP data and we explain why. The method of data normalization has a major impact on the quality of ChIP analyses. Therefore, we analyzed different normalization strategies, resulting in a thorough discussion of the advantages and drawbacks of the various approaches. CONCLUSION Here we provide a robust ChIP protocol and strategy to optimize the protocol for any type of tissue; we argue that quantitative real-time PCR (QPCR) is the best method to analyze the precipitates, and present comprehensive insights into data normalization.
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Affiliation(s)
- Max Haring
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
| | - Sascha Offermann
- Institute for Biology I, Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Tanja Danker
- Institute for Biology I, Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | - Ina Horst
- Institute for Biology I, Aachen University, Worringer Weg 1, 52074 Aachen, Germany
| | | | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Kruislaan 318, 1098 SM Amsterdam, The Netherlands
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Conconi A. The yeast rDNA locus: a model system to study DNA repair in chromatin. DNA Repair (Amst) 2007; 4:897-908. [PMID: 15996904 DOI: 10.1016/j.dnarep.2005.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/23/2022]
Abstract
Most of the studies on the effect of chromatin structure and chromatin remodeling on DNA repair are based on in vitro reconstituted assays. In such experiments individual nucleosomes are either released by nuclease digestion of native chromatin fibers or are assembled from purified histones. Though reconstituted assays are valid approaches to follow NER in chromatin they are of somehow limited physiological relevance since single core particles do not exist in vivo [K. van Holde, J. Zlatanova, The nucleosome core particle: does it have structural and physiological relevance? Bioessays 21 (1999) 776-778]. This is particularly true for studies involving core histones tails, as in their natural chromatin context histones tails participate in interactions that are not necessarily present in vitro [J.C. Hansen, C. Tse, A.P. Wolffe, Structure and function of the core histone N-termini: more than meets the eye, Biochemistry 37 (1998) 17637-17641; J.J. Hayes, J.C. Hansen, Nucleosomes and chromatin fiber, Curr. Opin. Genet. Dev. 11 (2001) 124-129]. Indeed it was found that human DNA ligase I has the capability to ligate a nick on the surface of a 215bp nucleosome but not a nick in a nucleosome lacking linker DNA, possibly because of forced interactions between histone tails and core DNA present in the latter complex [D.R. Chafin, J.M. Vitolo, L.A. Henricksen, B.A. Bambara, J.J. Hayes, Human DNA ligase I efficiently seals nicks in nucleosomes, EMBO J. 19 (2000) 5492-5501]. In addition, chromatin remodeling could also occur in the higher ordered folding of chromatin and involve multiple arrays of nucleosomes [P.J. Horn, C.L. Peterson, Chromatin higher order folding: wrapping up transcription, Science 297 (2002) 1824-1827]. By studying the chromatin structure of ribosomal genes in yeast, our knowledge of the fate of nucleosomes during transcription and DNA replication has improved considerably [R. Lucchini, J.M. Sogo, The dynamic structure of ribosomal RNA gene chromatin, in: M.R. Paule (Ed.), Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I, Springer-Verlag/R.G. Landes Company, 1998, pp. 254-276]. How nuclear processes such as DNA repair take place in chromatin is still largely unknown, and in this review I discuss how the yeast rDNA locus may be exploited to investigate DNA repair and chromatin modification in vivo.
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Affiliation(s)
- Antonio Conconi
- Department de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, 3001, 12(e) Avenue Nord, Sherbrooke, Que., Canada J1H 5N4
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Kodama Y, Nagaya S, Shinmyo A, Kato K. Mapping and characterization of DNase I hypersensitive sites in Arabidopsis chromatin. PLANT & CELL PHYSIOLOGY 2007; 48:459-70. [PMID: 17283013 DOI: 10.1093/pcp/pcm017] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Recent genome-wide analyses of yeast and human chromatin revealed the widespread prevalence of DNase I hypersensitive sites (DNase I HSs) at gene regulatory regions with possible roles in eukaryotic gene regulation. The presence of DNase I HSs in plants has been described for only a few genes, and we analyzed the chromatin structure of an 80 kb genomic region containing 30 variably expressed genes by DNase I sensitivity assay at 500 bp resolution in Arabidopsis. Distinct DNase I HSs were found at the 5' and/or 3' ends of most genes irrespective of their expression levels. Further analysis of well-characterized genes showed that the DNase I HSs occurred near cis-regulatory elements in the promoters of these genes. Upon transcriptional activation of a heat-inducible gene, the DNase I HS was extended into the vicinity of a cis-element and adjacent TATA element in the promoter. Concomitant with this change in DNase I HS, histones were acetylated, removed from the promoter, and a transcription activator bound to this cis-element. These results suggest that the DNase I HSs participate in the transcriptional regulation of Arabidopsis genes by enhancing the access of chromatin remodeling factors and/or transcription factors to their target sites as seen in yeast and human chromatin.
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Affiliation(s)
- Yuichi Kodama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
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Toussaint M, Levasseur G, Tremblay M, Paquette M, Conconi A. Psoralen photocrosslinking, a tool to study the chromatin structure of RNA polymerase I--transcribed ribosomal genes. Biochem Cell Biol 2005; 83:449-59. [PMID: 16094448 DOI: 10.1139/o05-141] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The chromatin structure of RNA polymerase I--transcribed ribosomal DNA (rDNA) is well characterized. In most organisms, i.e., lower eukaryotes, plants, and animals, only a fraction of ribosomal genes are transcriptionally active. At the chromatin level inactive rDNA is assembled into arrays of nucleosomes, whereas transcriptionally active rDNA does not contain canonical nucleosomes. To separate inactive (nucleosomal) and active (non-nucleosomal) rDNA, the technique of psoralen photocrosslinking has been used successfully both in vitro and in vivo. In Saccharomyces cerevisiae, the structure of rDNA chromatin has been particularly well studied during transcription and during DNA replication. Thus, the yeast rDNA locus has become a good model system to study the interplay of all nuclear DNA processes and chromatin. In this review we focused on the studies of chromatin in ribosomal genes and how these results have helped to address the fundamental question: What is the structure of chromatin in the coding regions of genes?
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Affiliation(s)
- Martin Toussaint
- Départment de Microbiologie et Infectiologie, Université de Sherbrooke, QC, Canada
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Metzler DE, Metzler CM, Sauke DJ. Transferring Groups by Displacement Reactions. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lightner J, Pearce G, Ryan CA, Browse J. Isolation of signaling mutants of tomato (Lycopersicon esculentum). MOLECULAR & GENERAL GENETICS : MGG 1993; 241:595-601. [PMID: 8264534 DOI: 10.1007/bf00279902] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
As a first step towards developing a genetic system for investigating signaling processes in plants, we have developed a screen for signaling mutants deficient in a wound response. We have isolated two mutants of tomato that lack detectable production of proteinase inhibitors induced systemically in leaves by wounding. The mutants are deficient in the induction of both proteinase Inhibitor I and proteinase Inhibitor II but can be induced to respond at near wild-type levels by methyl jasmonate, a known elicitor of inhibitor production in tomato. While completely deficient in systemic production of proteinase inhibitors, both mutants produce some proteinase inhibitor in wounded leaves. This evidence suggests the existence of two signaling pathways, one local and one systemic, that regulate the induction of proteinase inhibitor synthesis in response to wounding.
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Affiliation(s)
- J Lightner
- Institute of Biological Chemistry, Washington State University, Pullman 99164-6340
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